Job ID = 6455381 SRX = SRX287742 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:59:29 prefetch.2.10.7: 1) Downloading 'SRR869931'... 2020-06-21T09:59:29 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:02:32 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:02:32 prefetch.2.10.7: 1) 'SRR869931' was downloaded successfully Read 22109731 spots for SRR869931/SRR869931.sra Written 22109731 spots for SRR869931/SRR869931.sra fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:06:10 22109731 reads; of these: 22109731 (100.00%) were unpaired; of these: 1594102 (7.21%) aligned 0 times 13930091 (63.00%) aligned exactly 1 time 6585538 (29.79%) aligned >1 times 92.79% overall alignment rate Time searching: 00:06:10 Overall time: 00:06:10 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 1870 sequences. [bam_sort_core] merging from 12 files... [bam_rmdupse_core] 4221465 / 20515629 = 0.2058 in library ' ' BAM に変換しました。 Bed ファイルを作成中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sun, 21 Jun 2020 19:14:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287742/SRX287742.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287742/SRX287742.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287742/SRX287742.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287742/SRX287742.bam'] # control file = None # effective genome size = 1.20e+08 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-05 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Sun, 21 Jun 2020 19:14:54: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:14:54: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:14:59: 1000000 INFO @ Sun, 21 Jun 2020 19:15:04: 2000000 INFO @ Sun, 21 Jun 2020 19:15:09: 3000000 INFO @ Sun, 21 Jun 2020 19:15:14: 4000000 INFO @ Sun, 21 Jun 2020 19:15:19: 5000000 WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sun, 21 Jun 2020 19:15:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287742/SRX287742.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287742/SRX287742.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287742/SRX287742.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287742/SRX287742.bam'] # control file = None # effective genome size = 1.20e+08 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-10 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Sun, 21 Jun 2020 19:15:24: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:15:24: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:15:25: 6000000 INFO @ Sun, 21 Jun 2020 19:15:29: 1000000 INFO @ Sun, 21 Jun 2020 19:15:30: 7000000 INFO @ Sun, 21 Jun 2020 19:15:35: 2000000 INFO @ Sun, 21 Jun 2020 19:15:36: 8000000 INFO @ Sun, 21 Jun 2020 19:15:41: 3000000 INFO @ Sun, 21 Jun 2020 19:15:41: 9000000 INFO @ Sun, 21 Jun 2020 19:15:46: 4000000 INFO @ Sun, 21 Jun 2020 19:15:47: 10000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sun, 21 Jun 2020 19:15:52: 5000000 INFO @ Sun, 21 Jun 2020 19:15:53: 11000000 INFO @ Sun, 21 Jun 2020 19:15:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287742/SRX287742.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287742/SRX287742.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287742/SRX287742.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287742/SRX287742.bam'] # control file = None # effective genome size = 1.20e+08 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-20 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Sun, 21 Jun 2020 19:15:54: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:15:54: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:15:58: 6000000 INFO @ Sun, 21 Jun 2020 19:15:58: 12000000 INFO @ Sun, 21 Jun 2020 19:15:59: 1000000 INFO @ Sun, 21 Jun 2020 19:16:03: 7000000 INFO @ Sun, 21 Jun 2020 19:16:04: 13000000 INFO @ Sun, 21 Jun 2020 19:16:05: 2000000 INFO @ Sun, 21 Jun 2020 19:16:09: 8000000 INFO @ Sun, 21 Jun 2020 19:16:10: 14000000 INFO @ Sun, 21 Jun 2020 19:16:11: 3000000 INFO @ Sun, 21 Jun 2020 19:16:15: 9000000 INFO @ Sun, 21 Jun 2020 19:16:16: 15000000 INFO @ Sun, 21 Jun 2020 19:16:16: 4000000 INFO @ Sun, 21 Jun 2020 19:16:21: 10000000 INFO @ Sun, 21 Jun 2020 19:16:22: 16000000 INFO @ Sun, 21 Jun 2020 19:16:22: 5000000 INFO @ Sun, 21 Jun 2020 19:16:24: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:16:24: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:16:24: #1 total tags in treatment: 16294164 INFO @ Sun, 21 Jun 2020 19:16:24: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:16:24: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 19:16:24: #1 tags after filtering in treatment: 16294164 INFO @ Sun, 21 Jun 2020 19:16:24: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:16:24: #1 finished! INFO @ Sun, 21 Jun 2020 19:16:24: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:16:24: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:16:25: #2 number of paired peaks: 723 WARNING @ Sun, 21 Jun 2020 19:16:25: Fewer paired peaks (723) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 723 pairs to build model! INFO @ Sun, 21 Jun 2020 19:16:25: start model_add_line... INFO @ Sun, 21 Jun 2020 19:16:25: start X-correlation... INFO @ Sun, 21 Jun 2020 19:16:25: end of X-cor INFO @ Sun, 21 Jun 2020 19:16:25: #2 finished! INFO @ Sun, 21 Jun 2020 19:16:25: #2 predicted fragment length is 29 bps INFO @ Sun, 21 Jun 2020 19:16:25: #2 alternative fragment length(s) may be 3,29 bps INFO @ Sun, 21 Jun 2020 19:16:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287742/SRX287742.05_model.r WARNING @ Sun, 21 Jun 2020 19:16:25: #2 Since the d (29) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:16:25: #2 You may need to consider one of the other alternative d(s): 3,29 WARNING @ Sun, 21 Jun 2020 19:16:25: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 19:16:25: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:16:25: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:16:26: 11000000 INFO @ Sun, 21 Jun 2020 19:16:28: 6000000 INFO @ Sun, 21 Jun 2020 19:16:32: 12000000 INFO @ Sun, 21 Jun 2020 19:16:33: 7000000 INFO @ Sun, 21 Jun 2020 19:16:38: 13000000 INFO @ Sun, 21 Jun 2020 19:16:39: 8000000 INFO @ Sun, 21 Jun 2020 19:16:44: 14000000 INFO @ Sun, 21 Jun 2020 19:16:45: 9000000 INFO @ Sun, 21 Jun 2020 19:16:49: 15000000 INFO @ Sun, 21 Jun 2020 19:16:51: 10000000 INFO @ Sun, 21 Jun 2020 19:16:55: 16000000 INFO @ Sun, 21 Jun 2020 19:16:56: 11000000 INFO @ Sun, 21 Jun 2020 19:16:56: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:16:57: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:16:57: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:16:57: #1 total tags in treatment: 16294164 INFO @ Sun, 21 Jun 2020 19:16:57: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:16:57: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 19:16:58: #1 tags after filtering in treatment: 16294164 INFO @ Sun, 21 Jun 2020 19:16:58: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:16:58: #1 finished! INFO @ Sun, 21 Jun 2020 19:16:58: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:16:58: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:16:59: #2 number of paired peaks: 723 WARNING @ Sun, 21 Jun 2020 19:16:59: Fewer paired peaks (723) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 723 pairs to build model! INFO @ Sun, 21 Jun 2020 19:16:59: start model_add_line... INFO @ Sun, 21 Jun 2020 19:16:59: start X-correlation... INFO @ Sun, 21 Jun 2020 19:16:59: end of X-cor INFO @ Sun, 21 Jun 2020 19:16:59: #2 finished! INFO @ Sun, 21 Jun 2020 19:16:59: #2 predicted fragment length is 29 bps INFO @ Sun, 21 Jun 2020 19:16:59: #2 alternative fragment length(s) may be 3,29 bps INFO @ Sun, 21 Jun 2020 19:16:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287742/SRX287742.10_model.r WARNING @ Sun, 21 Jun 2020 19:16:59: #2 Since the d (29) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:16:59: #2 You may need to consider one of the other alternative d(s): 3,29 WARNING @ Sun, 21 Jun 2020 19:16:59: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 19:16:59: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:16:59: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:17:02: 12000000 INFO @ Sun, 21 Jun 2020 19:17:08: 13000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:17:12: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287742/SRX287742.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:17:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287742/SRX287742.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:17:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287742/SRX287742.05_summits.bed INFO @ Sun, 21 Jun 2020 19:17:12: Done! pass1 - making usageList (635 chroms): 1 millis pass2 - checking and writing primary data (2477 records, 4 fields): 18 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:17:13: 14000000 INFO @ Sun, 21 Jun 2020 19:17:19: 15000000 INFO @ Sun, 21 Jun 2020 19:17:24: 16000000 INFO @ Sun, 21 Jun 2020 19:17:26: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:17:26: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:17:26: #1 total tags in treatment: 16294164 INFO @ Sun, 21 Jun 2020 19:17:26: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:17:26: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 19:17:27: #1 tags after filtering in treatment: 16294164 INFO @ Sun, 21 Jun 2020 19:17:27: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:17:27: #1 finished! INFO @ Sun, 21 Jun 2020 19:17:27: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:17:27: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:17:28: #2 number of paired peaks: 723 WARNING @ Sun, 21 Jun 2020 19:17:28: Fewer paired peaks (723) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 723 pairs to build model! INFO @ Sun, 21 Jun 2020 19:17:28: start model_add_line... INFO @ Sun, 21 Jun 2020 19:17:28: start X-correlation... INFO @ Sun, 21 Jun 2020 19:17:28: end of X-cor INFO @ Sun, 21 Jun 2020 19:17:28: #2 finished! INFO @ Sun, 21 Jun 2020 19:17:28: #2 predicted fragment length is 29 bps INFO @ Sun, 21 Jun 2020 19:17:28: #2 alternative fragment length(s) may be 3,29 bps INFO @ Sun, 21 Jun 2020 19:17:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287742/SRX287742.20_model.r WARNING @ Sun, 21 Jun 2020 19:17:28: #2 Since the d (29) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:17:28: #2 You may need to consider one of the other alternative d(s): 3,29 WARNING @ Sun, 21 Jun 2020 19:17:28: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 19:17:28: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:17:28: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:17:30: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:17:45: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287742/SRX287742.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:17:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287742/SRX287742.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:17:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287742/SRX287742.10_summits.bed INFO @ Sun, 21 Jun 2020 19:17:45: Done! pass1 - making usageList (513 chroms): 2 millis pass2 - checking and writing primary data (2042 records, 4 fields): 16 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 19:17:58: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:18:13: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287742/SRX287742.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:18:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287742/SRX287742.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:18:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287742/SRX287742.20_summits.bed INFO @ Sun, 21 Jun 2020 19:18:13: Done! pass1 - making usageList (302 chroms): 1 millis pass2 - checking and writing primary data (650 records, 4 fields): 10 millis CompletedMACS2peakCalling